Starting phenix.real_space_refine on Thu Dec 7 22:40:28 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sl8_25194/12_2023/7sl8_25194_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sl8_25194/12_2023/7sl8_25194.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sl8_25194/12_2023/7sl8_25194.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sl8_25194/12_2023/7sl8_25194.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sl8_25194/12_2023/7sl8_25194_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sl8_25194/12_2023/7sl8_25194_neut_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 34 5.16 5 C 3493 2.51 5 N 844 2.21 5 O 924 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 133": "NH1" <-> "NH2" Residue "A ARG 135": "NH1" <-> "NH2" Residue "A ARG 140": "NH1" <-> "NH2" Residue "A GLU 225": "OE1" <-> "OE2" Residue "A ARG 267": "NH1" <-> "NH2" Residue "A GLU 372": "OE1" <-> "OE2" Residue "A ARG 379": "NH1" <-> "NH2" Residue "A GLU 482": "OE1" <-> "OE2" Residue "A GLU 513": "OE1" <-> "OE2" Residue "A ARG 642": "NH1" <-> "NH2" Residue "B ARG 100": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 5295 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 582, 4362 Classifications: {'peptide': 582} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 22, 'TRANS': 559} Chain breaks: 2 Unresolved non-hydrogen bonds: 179 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 158 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 92 Chain: "B" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 905 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 114} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.63, per 1000 atoms: 0.69 Number of scatterers: 5295 At special positions: 0 Unit cell: (109.18, 78.44, 90.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 34 16.00 O 924 8.00 N 844 7.00 C 3493 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 255 " - pdb=" SG CYS A 511 " distance=2.04 Simple disulfide: pdb=" SG CYS A 345 " - pdb=" SG CYS A 351 " distance=2.02 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 517 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 24 " - pdb=" SG CYS B 97 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.75 Conformation dependent library (CDL) restraints added in 1.3 seconds 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1284 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 3 sheets defined 55.7% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 26 through 48 removed outlier: 3.513A pdb=" N SER A 30 " --> pdb=" O ALA A 26 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N VAL A 31 " --> pdb=" O ALA A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 75 removed outlier: 3.900A pdb=" N SER A 73 " --> pdb=" O PRO A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 93 Processing helix chain 'A' and resid 97 through 114 removed outlier: 3.559A pdb=" N LEU A 108 " --> pdb=" O ALA A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 122 Processing helix chain 'A' and resid 128 through 133 Processing helix chain 'A' and resid 139 through 156 Processing helix chain 'A' and resid 158 through 173 Processing helix chain 'A' and resid 177 through 194 Processing helix chain 'A' and resid 202 through 226 Processing helix chain 'A' and resid 230 through 237 removed outlier: 3.582A pdb=" N TYR A 236 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N MET A 237 " --> pdb=" O MET A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 256 No H-bonds generated for 'chain 'A' and resid 253 through 256' Processing helix chain 'A' and resid 276 through 293 removed outlier: 3.779A pdb=" N CYS A 292 " --> pdb=" O LEU A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 302 Processing helix chain 'A' and resid 307 through 328 removed outlier: 3.651A pdb=" N LEU A 322 " --> pdb=" O GLY A 318 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LEU A 323 " --> pdb=" O TYR A 319 " (cutoff:3.500A) Proline residue: A 324 - end of helix Processing helix chain 'A' and resid 330 through 338 Processing helix chain 'A' and resid 348 through 354 removed outlier: 4.692A pdb=" N LYS A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 370 removed outlier: 4.500A pdb=" N TYR A 366 " --> pdb=" O ASN A 363 " (cutoff:3.500A) Proline residue: A 367 - end of helix Processing helix chain 'A' and resid 379 through 408 removed outlier: 3.569A pdb=" N LEU A 383 " --> pdb=" O ARG A 379 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU A 387 " --> pdb=" O LEU A 383 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LEU A 390 " --> pdb=" O MET A 386 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N SER A 393 " --> pdb=" O ALA A 389 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ILE A 397 " --> pdb=" O SER A 393 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASN A 399 " --> pdb=" O THR A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 413 No H-bonds generated for 'chain 'A' and resid 410 through 413' Processing helix chain 'A' and resid 419 through 439 removed outlier: 3.504A pdb=" N ALA A 439 " --> pdb=" O VAL A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 444 No H-bonds generated for 'chain 'A' and resid 441 through 444' Processing helix chain 'A' and resid 453 through 476 removed outlier: 3.991A pdb=" N SER A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N TYR A 462 " --> pdb=" O SER A 458 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU A 463 " --> pdb=" O VAL A 459 " (cutoff:3.500A) Proline residue: A 465 - end of helix Processing helix chain 'A' and resid 482 through 504 removed outlier: 3.863A pdb=" N TRP A 487 " --> pdb=" O GLN A 483 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N SER A 498 " --> pdb=" O LEU A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 522 No H-bonds generated for 'chain 'A' and resid 519 through 522' Processing helix chain 'A' and resid 528 through 547 Processing helix chain 'A' and resid 553 through 555 No H-bonds generated for 'chain 'A' and resid 553 through 555' Processing helix chain 'A' and resid 639 through 665 Processing sheet with id= A, first strand: chain 'B' and resid 5 through 9 removed outlier: 3.575A pdb=" N GLN B 5 " --> pdb=" O SER B 27 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER B 23 " --> pdb=" O SER B 9 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N THR B 79 " --> pdb=" O ASP B 74 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP B 74 " --> pdb=" O THR B 79 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 13 through 15 removed outlier: 6.502A pdb=" N THR B 117 " --> pdb=" O VAL B 14 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 39 through 41 271 hydrogen bonds defined for protein. 756 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.35 Time building geometry restraints manager: 2.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1579 1.34 - 1.46: 1073 1.46 - 1.58: 2721 1.58 - 1.69: 0 1.69 - 1.81: 53 Bond restraints: 5426 Sorted by residual: bond pdb=" C LEU A 323 " pdb=" N PRO A 324 " ideal model delta sigma weight residual 1.334 1.405 -0.071 2.34e-02 1.83e+03 9.11e+00 bond pdb=" C TRP A 276 " pdb=" N PRO A 277 " ideal model delta sigma weight residual 1.334 1.374 -0.040 2.34e-02 1.83e+03 2.96e+00 bond pdb=" C13 CLR A 701 " pdb=" C17 CLR A 701 " ideal model delta sigma weight residual 1.550 1.517 0.033 2.00e-02 2.50e+03 2.70e+00 bond pdb=" C10 CLR A 701 " pdb=" C9 CLR A 701 " ideal model delta sigma weight residual 1.551 1.519 0.032 2.00e-02 2.50e+03 2.50e+00 bond pdb=" C VAL A 117 " pdb=" N PRO A 118 " ideal model delta sigma weight residual 1.335 1.354 -0.019 1.28e-02 6.10e+03 2.27e+00 ... (remaining 5421 not shown) Histogram of bond angle deviations from ideal: 99.41 - 106.40: 146 106.40 - 113.38: 2961 113.38 - 120.37: 2214 120.37 - 127.35: 2023 127.35 - 134.34: 68 Bond angle restraints: 7412 Sorted by residual: angle pdb=" N VAL A 359 " pdb=" CA VAL A 359 " pdb=" C VAL A 359 " ideal model delta sigma weight residual 108.12 118.97 -10.85 1.44e+00 4.82e-01 5.68e+01 angle pdb=" N VAL A 329 " pdb=" CA VAL A 329 " pdb=" C VAL A 329 " ideal model delta sigma weight residual 113.71 109.05 4.66 9.50e-01 1.11e+00 2.40e+01 angle pdb=" N LEU A 527 " pdb=" CA LEU A 527 " pdb=" C LEU A 527 " ideal model delta sigma weight residual 113.55 108.18 5.37 1.26e+00 6.30e-01 1.82e+01 angle pdb=" N LYS A 358 " pdb=" CA LYS A 358 " pdb=" C LYS A 358 " ideal model delta sigma weight residual 111.28 115.50 -4.22 1.09e+00 8.42e-01 1.50e+01 angle pdb=" N ALA A 464 " pdb=" CA ALA A 464 " pdb=" C ALA A 464 " ideal model delta sigma weight residual 109.81 118.33 -8.52 2.21e+00 2.05e-01 1.49e+01 ... (remaining 7407 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.96: 2754 15.96 - 31.92: 332 31.92 - 47.87: 83 47.87 - 63.83: 8 63.83 - 79.79: 4 Dihedral angle restraints: 3181 sinusoidal: 1172 harmonic: 2009 Sorted by residual: dihedral pdb=" CA PRO A 518 " pdb=" C PRO A 518 " pdb=" N THR A 519 " pdb=" CA THR A 519 " ideal model delta harmonic sigma weight residual -180.00 -158.39 -21.61 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA TYR B 101 " pdb=" C TYR B 101 " pdb=" N THR B 102 " pdb=" CA THR B 102 " ideal model delta harmonic sigma weight residual 180.00 -158.40 -21.60 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA TYR B 61 " pdb=" C TYR B 61 " pdb=" N ALA B 62 " pdb=" CA ALA B 62 " ideal model delta harmonic sigma weight residual 180.00 158.68 21.32 0 5.00e+00 4.00e-02 1.82e+01 ... (remaining 3178 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 652 0.055 - 0.109: 180 0.109 - 0.164: 38 0.164 - 0.218: 12 0.218 - 0.273: 2 Chirality restraints: 884 Sorted by residual: chirality pdb=" C13 CLR A 701 " pdb=" C12 CLR A 701 " pdb=" C14 CLR A 701 " pdb=" C17 CLR A 701 " both_signs ideal model delta sigma weight residual False -2.93 -2.66 -0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA CYS A 361 " pdb=" N CYS A 361 " pdb=" C CYS A 361 " pdb=" CB CYS A 361 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CB VAL A 98 " pdb=" CA VAL A 98 " pdb=" CG1 VAL A 98 " pdb=" CG2 VAL A 98 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 881 not shown) Planarity restraints: 902 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 465 " 0.044 5.00e-02 4.00e+02 6.59e-02 6.94e+00 pdb=" N PRO A 466 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 466 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 466 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 330 " 0.040 5.00e-02 4.00e+02 5.99e-02 5.74e+00 pdb=" N PRO A 331 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 331 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 331 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 102 " 0.037 5.00e-02 4.00e+02 5.66e-02 5.12e+00 pdb=" N PRO B 103 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO B 103 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 103 " 0.032 5.00e-02 4.00e+02 ... (remaining 899 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 1752 2.83 - 3.35: 4932 3.35 - 3.87: 8781 3.87 - 4.38: 9502 4.38 - 4.90: 16815 Nonbonded interactions: 41782 Sorted by model distance: nonbonded pdb=" OE2 GLU A 234 " pdb=" OH TYR B 101 " model vdw 2.316 2.440 nonbonded pdb=" O SER A 446 " pdb=" OG SER A 446 " model vdw 2.321 2.440 nonbonded pdb=" O LEU A 152 " pdb=" OG1 THR A 156 " model vdw 2.327 2.440 nonbonded pdb=" CD2 TYR A 319 " pdb=" C24 CLR A 701 " model vdw 2.330 3.740 nonbonded pdb=" O LEU A 190 " pdb=" OG1 THR A 194 " model vdw 2.342 2.440 ... (remaining 41777 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.70 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 1.930 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.730 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 5426 Z= 0.358 Angle : 0.968 10.854 7412 Z= 0.543 Chirality : 0.057 0.273 884 Planarity : 0.008 0.066 902 Dihedral : 14.662 79.791 1882 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 0.92 % Allowed : 11.28 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.09 (0.25), residues: 692 helix: -2.46 (0.19), residues: 413 sheet: -2.41 (0.66), residues: 49 loop : -2.90 (0.36), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 68 HIS 0.003 0.001 HIS A 525 PHE 0.016 0.002 PHE B 49 TYR 0.010 0.002 TYR A 144 ARG 0.004 0.001 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 126 time to evaluate : 0.599 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 131 average time/residue: 0.1965 time to fit residues: 32.6856 Evaluate side-chains 97 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 95 time to evaluate : 0.600 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0520 time to fit residues: 1.0066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 58 optimal weight: 6.9990 chunk 52 optimal weight: 0.2980 chunk 29 optimal weight: 0.4980 chunk 17 optimal weight: 0.3980 chunk 35 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 20 optimal weight: 0.6980 chunk 32 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS A 142 GLN A 448 GLN A 525 HIS A 648 ASN ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5426 Z= 0.169 Angle : 0.616 7.551 7412 Z= 0.318 Chirality : 0.039 0.144 884 Planarity : 0.005 0.049 902 Dihedral : 5.595 53.003 811 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 2.22 % Allowed : 17.93 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.30), residues: 692 helix: -0.45 (0.25), residues: 397 sheet: -1.96 (0.66), residues: 48 loop : -2.77 (0.35), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 289 HIS 0.002 0.000 HIS B 121 PHE 0.015 0.001 PHE A 432 TYR 0.021 0.001 TYR B 61 ARG 0.004 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 108 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 10 residues processed: 114 average time/residue: 0.1580 time to fit residues: 24.0017 Evaluate side-chains 103 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 93 time to evaluate : 0.605 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0557 time to fit residues: 1.8128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 34 optimal weight: 0.9980 chunk 19 optimal weight: 0.0980 chunk 52 optimal weight: 6.9990 chunk 42 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 666 ASN ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5426 Z= 0.168 Angle : 0.585 7.615 7412 Z= 0.298 Chirality : 0.039 0.148 884 Planarity : 0.004 0.044 902 Dihedral : 5.473 59.283 811 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 3.51 % Allowed : 18.85 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.32), residues: 692 helix: 0.17 (0.27), residues: 403 sheet: -1.45 (0.69), residues: 48 loop : -2.59 (0.37), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 68 HIS 0.001 0.000 HIS A 525 PHE 0.018 0.001 PHE A 658 TYR 0.015 0.001 TYR B 61 ARG 0.006 0.000 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 103 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 5 residues processed: 116 average time/residue: 0.1501 time to fit residues: 23.2935 Evaluate side-chains 96 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 91 time to evaluate : 0.616 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0518 time to fit residues: 1.2642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 32 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 62 optimal weight: 8.9990 chunk 66 optimal weight: 0.8980 chunk 59 optimal weight: 10.0000 chunk 17 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 525 HIS ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5426 Z= 0.188 Angle : 0.607 8.800 7412 Z= 0.302 Chirality : 0.039 0.154 884 Planarity : 0.004 0.042 902 Dihedral : 5.595 59.187 811 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 3.70 % Allowed : 20.70 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.33), residues: 692 helix: 0.53 (0.27), residues: 396 sheet: -0.95 (0.73), residues: 48 loop : -2.46 (0.37), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 68 HIS 0.002 0.000 HIS A 525 PHE 0.020 0.001 PHE B 69 TYR 0.013 0.001 TYR B 61 ARG 0.003 0.000 ARG B 47 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 102 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 11 residues processed: 117 average time/residue: 0.1481 time to fit residues: 23.2979 Evaluate side-chains 101 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 90 time to evaluate : 0.591 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0555 time to fit residues: 1.8618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 34 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 chunk 60 optimal weight: 0.4980 chunk 13 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 HIS A 525 HIS ** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5426 Z= 0.225 Angle : 0.617 8.549 7412 Z= 0.312 Chirality : 0.040 0.160 884 Planarity : 0.004 0.044 902 Dihedral : 5.497 58.717 811 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 2.40 % Allowed : 24.40 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.33), residues: 692 helix: 0.67 (0.27), residues: 397 sheet: -0.70 (0.74), residues: 48 loop : -2.30 (0.38), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 68 HIS 0.008 0.001 HIS A 224 PHE 0.012 0.001 PHE B 69 TYR 0.011 0.001 TYR B 61 ARG 0.004 0.000 ARG B 47 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 95 time to evaluate : 0.642 Fit side-chains outliers start: 13 outliers final: 7 residues processed: 103 average time/residue: 0.1711 time to fit residues: 23.2942 Evaluate side-chains 94 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 87 time to evaluate : 0.610 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0553 time to fit residues: 1.4993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 39 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 66 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 chunk 30 optimal weight: 0.4980 chunk 5 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 35 optimal weight: 0.0370 chunk 64 optimal weight: 0.0670 chunk 7 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 525 HIS A 648 ASN ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5426 Z= 0.157 Angle : 0.615 10.637 7412 Z= 0.303 Chirality : 0.039 0.174 884 Planarity : 0.004 0.044 902 Dihedral : 5.259 55.565 811 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.77 % Allowed : 25.32 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.33), residues: 692 helix: 0.86 (0.27), residues: 403 sheet: -0.46 (0.75), residues: 48 loop : -2.21 (0.39), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 660 HIS 0.002 0.000 HIS A 525 PHE 0.014 0.001 PHE B 69 TYR 0.017 0.001 TYR B 61 ARG 0.004 0.000 ARG B 47 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 108 time to evaluate : 0.554 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 6 residues processed: 115 average time/residue: 0.1528 time to fit residues: 23.6104 Evaluate side-chains 94 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 88 time to evaluate : 0.568 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1094 time to fit residues: 1.7550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 48 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 26 optimal weight: 0.4980 chunk 39 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 HIS ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5426 Z= 0.178 Angle : 0.628 14.395 7412 Z= 0.308 Chirality : 0.040 0.242 884 Planarity : 0.004 0.039 902 Dihedral : 5.270 55.647 811 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.66 % Allowed : 26.62 % Favored : 71.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.34), residues: 692 helix: 1.02 (0.27), residues: 402 sheet: -0.24 (0.79), residues: 48 loop : -2.12 (0.40), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 68 HIS 0.004 0.001 HIS A 224 PHE 0.020 0.001 PHE A 168 TYR 0.010 0.001 TYR B 61 ARG 0.004 0.000 ARG B 47 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 96 time to evaluate : 0.563 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 103 average time/residue: 0.1550 time to fit residues: 21.2324 Evaluate side-chains 97 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 91 time to evaluate : 0.551 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0980 time to fit residues: 1.5803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 12 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 52 optimal weight: 0.7980 chunk 60 optimal weight: 0.1980 chunk 63 optimal weight: 6.9990 chunk 58 optimal weight: 9.9990 chunk 61 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5426 Z= 0.183 Angle : 0.641 14.196 7412 Z= 0.310 Chirality : 0.039 0.153 884 Planarity : 0.004 0.040 902 Dihedral : 5.165 55.235 811 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 1.66 % Allowed : 25.88 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.34), residues: 692 helix: 1.23 (0.28), residues: 396 sheet: -0.10 (0.80), residues: 48 loop : -2.13 (0.39), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 660 HIS 0.004 0.001 HIS A 525 PHE 0.012 0.001 PHE B 69 TYR 0.011 0.001 TYR A 144 ARG 0.004 0.000 ARG B 47 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 95 time to evaluate : 0.614 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 98 average time/residue: 0.1454 time to fit residues: 19.5116 Evaluate side-chains 96 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 89 time to evaluate : 0.600 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0563 time to fit residues: 1.5026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 26 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 58 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 HIS ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 5426 Z= 0.319 Angle : 0.709 13.760 7412 Z= 0.352 Chirality : 0.043 0.178 884 Planarity : 0.004 0.043 902 Dihedral : 5.469 57.838 811 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 1.48 % Allowed : 26.62 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.34), residues: 692 helix: 1.09 (0.28), residues: 396 sheet: -0.11 (0.80), residues: 48 loop : -2.17 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 68 HIS 0.004 0.001 HIS A 224 PHE 0.015 0.002 PHE A 534 TYR 0.015 0.002 TYR A 144 ARG 0.004 0.000 ARG B 47 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 83 time to evaluate : 0.552 Fit side-chains outliers start: 8 outliers final: 8 residues processed: 90 average time/residue: 0.1518 time to fit residues: 18.6027 Evaluate side-chains 89 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 81 time to evaluate : 0.600 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0590 time to fit residues: 1.6438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 68 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 58 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5426 Z= 0.203 Angle : 0.650 14.084 7412 Z= 0.321 Chirality : 0.041 0.159 884 Planarity : 0.004 0.041 902 Dihedral : 5.304 55.573 811 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.37 % Allowed : 27.54 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.34), residues: 692 helix: 1.18 (0.28), residues: 397 sheet: -0.38 (0.76), residues: 48 loop : -2.19 (0.40), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 487 HIS 0.003 0.001 HIS A 525 PHE 0.010 0.001 PHE A 432 TYR 0.012 0.001 TYR B 61 ARG 0.004 0.000 ARG B 47 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 89 time to evaluate : 0.598 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 90 average time/residue: 0.1408 time to fit residues: 17.5858 Evaluate side-chains 87 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 86 time to evaluate : 0.625 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0555 time to fit residues: 0.9226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 15 optimal weight: 5.9990 chunk 54 optimal weight: 9.9990 chunk 22 optimal weight: 0.2980 chunk 56 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.129966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.109413 restraints weight = 9886.694| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 2.74 r_work: 0.3595 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3612 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3612 r_free = 0.3612 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3611 r_free = 0.3611 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3611 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5426 Z= 0.182 Angle : 0.646 13.968 7412 Z= 0.315 Chirality : 0.040 0.166 884 Planarity : 0.004 0.040 902 Dihedral : 5.147 54.902 811 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.74 % Allowed : 27.73 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.34), residues: 692 helix: 1.33 (0.28), residues: 398 sheet: -0.38 (0.73), residues: 48 loop : -2.14 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 660 HIS 0.002 0.001 HIS A 525 PHE 0.014 0.001 PHE B 49 TYR 0.012 0.001 TYR B 61 ARG 0.004 0.000 ARG B 47 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1462.79 seconds wall clock time: 27 minutes 4.77 seconds (1624.77 seconds total)